tbuckley/cabot-search huggingface dataset:
Abstract 6306: Genomic analysis markers of stemness in oral cancer progression
Authors: Gretchen Unger, Beverly G. Wuertz, Patrick Gaffney, Frank G. Ondrey
Journal: Cancer Research (2022)

Abstract Introduction: In clinical cancer treatment there is an continuing effort to identify limited gene sets from high dimensional data to predict risk, treatment response, etc. Oral carcinogenesis is a multistep process of mutations, disordered growth, and the development of invasion. In the oral cancer milieu, inflammation and stemness has been demonstrated to be cooperative during carcinogenesis. We hypothesized that differences in inflammation, stemness, and EMT might distinguish lesion and adjacent normal mucosa in our RNA Seq data on preneoplastic lesions. Once candidate genes are identified they might be applied to other oral mucosal specimens to identify risk for malignancy development. Materials and Methods: We collected lesion and adjacent normal mucosal tissues from 16 subjects with high risk leukoplakia and early oral cancer (T1N0 and T2N0). Sequencing libraries were generated using the Illumina Truseq Stranded mRNA library prep kit. Sequencing was performed on an Illumina Hiseq 3000 instrument with paired-end 75bp read and sequenced to an overall depth of 30 million reads per sample. Results: After developing a biospecimen collection procedure that functions in the senior author’s clinic flow, we were able to isolate sequenceable total RNA from 100% of the specimens we collected. We identified several hundred differentially expressed genes between lesion and adjacent normal. With regard to stemness, inflammation, and EMT we multiple candidate genes that could be incorporated into a limited gene set for further studies. Aldehyde dehydrogenase family members were of particular interest in the stemness candidate genes, for example. ALD 1A1 and ALD 3B1, were significantly upregulated in lesion versus normal (P&amp;lt; 0.02). Conclusions: We conclude there are differentially expressed inflammatory, EMT, and stemness in oral preneoplastic specimens. We have identified multiple candidate genes that could be assembled into a limited gene panel (12-24 genes) for further studies of oral cancer risk in mucosal lesions Citation Format: Gretchen Unger, Beverly G. Wuertz, Patrick Gaffney, Frank G. Ondrey. Genomic analysis markers of stemness in oral cancer progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6306.
Abstract 889: NF-κB-mediated mitophagy contributes to the maintenance of cancer stem cells in ovarian cancer
Authors: Na Li, Tejinder Pal, Shurui Cai, Ananya Banerjee, Xuetao Bai, Kousalya Lavudi, Qi-En Wang
Journal: Cancer Research (2022)

Abstract Tumors contain phenotypically and functionally heterogeneous cancer cells. Among them, a minority of cell subpopulation, termed cancer stem cells (CSCs), which possess the self-renewal capacity and are able to generate the heterogeneous lineage of cancer cells, has been believed to be responsible for the initiation and progression of the tumor. However, it is still unclear how the stemness properties of CSCs are maintained in the tumor. Mitophagy is a process by which damaged mitochondria are cleared via autophagy. The significance of mitophagy in the maintenance of CSC has been investigated in multiple CSC types. Our recent study shows that ovarian CSCs also exhibit enhanced mitophagy, which is mainly attributed to elevated expression of mitophagy receptors BNIP3 and BNIP3L. Downregulation of BNIP3 or BNIP3L significantly diminished mitophagy in ovarian CSCs and compromised their self-renewal capability. Mechanistic investigation further revealed that enhanced NF-κB signaling contributes to the increased expression of BNIP3 and BNIP3L. Inhibition of NF-κB signaling pathway via p65 knockdown or specific inhibitors is able to reduce mitophagy in ovarian CSCs. In summary, our data suggest that selective inhibition of NF-κB is able to deplete CSCs by interfering with mitochondria quality control in these cells and has potential to prevent tumor relapse and metastasis. Citation Format: Na Li, Tejinder Pal, Shurui Cai, Ananya Banerjee, Xuetao Bai, Kousalya Lavudi, Qi-En Wang. NF-κB-mediated mitophagy contributes to the maintenance of cancer stem cells in ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 889.
Abstract 3323: Discovery of a small-molecule inhibitor that can target EGFR with C797S mutation
Authors: Dongsu Kim, Woo Seung Son, Anna Jang, Yeri Lee, Donggeon Kim, Changyu Choi, Kyung Hoon Min, Sung Pil Choi, Sang Kyun Lim
Journal: Cancer Research (2022)

Abstract EGFR is a transmembrane protein that functions as a receptor tyrosine kinase (RTK). Upon ligand binding or by activating mutations (Exon19 deletion, L858R mutation, and others), EGFR turns on the downstream signals that include oncogenic RAS/MEK/ERK, PI3K/AKT/mTOR, and JAK/STAT pathways. EGFR gene mutations and amplifications are frequently found in various human cancers and, in non-small cell lung cancer (NSCLC), the EGFR gene is mutated with 10-15% frequency (about 50% in Asian patients). While the 1st and 2nd generation EGFR inhibitors are effective in targeting EGFR mutants with Exon19 deletion and L858R mutation, additional T790M mutation in the EGFR gene causes resistance. The 3rd generation EGFR inhibitor (Osimertinib) works against EGFR mutants with T790M mutation; however, another EGFR mutation occurs at the amino acid 797 position (C797S), which makes Osimertinib ineffective. This is one of the major resistance mechanisms in Osimertinib-treated patients, and the 4th generation EGFR inhibitor that can target the C797S mutant is needed. We developed a compound that effectively disables various EGFR mutations, including Del19/T790M/C797S, L858R/T790/C797S, Del19/C797S, and L858R/C797S. In vitro kinase assay and cellular assays showed high potency and selectivity. In vivo PK/PD and efficacy tests confirmed the great therapeutic potential of this inhibitor for patients with EGFR mutations. Citation Format: Dongsu Kim, Woo Seung Son, Anna Jang, Yeri Lee, Donggeon Kim, Changyu Choi, Kyung Hoon Min, Sung Pil Choi, Sang Kyun Lim. Discovery of a small-molecule inhibitor that can target EGFR with C797S mutation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3323.
Abstract 2763: Adaptation of therapeutic NK cell line to tumor microenvironment culture conditions increases potency and reduces cellular exhaustion
Authors: Ann Lu, Yunmin Li, Albert Wong, James Lim
Journal: Cancer Research (2022)

Abstract NK-92 is a well-characterized human NK cell line that has demonstrated promising anti-cancer activities in clinical trials. However, the immunosuppressive solid tumor microenvironment (TME) can inhibit NK-92 function thereby limiting its cytolytic properties against tumor cells. To address this limitation, we serially passaged and maintained NK-92 cell lines under tumor microenvironment culture conditions (2.0 PSI + 1% O2) for a minimum of 5+ weeks. This adaptation period was used to precondition and expand NK cells with lower oxygen dependency, enriching for subset of cells that have metabolically adapted to pressurized and hypoxic culture conditions. NK cells maintained and expanded under TME culture conditions gradually reduced their cell-doubling times to reach parity with parental lines maintained under ambient oxygen (21% O2) culture conditions. This adaptation period coincided with improved tumor killing properties for TME-Adapted NK cells (TANK) against the non-small cell lung cancer cell line, A549. Enhanced cytolytic activity of TANK cells was two-fold greater than their non-TME adapted counterparts, with sustained potency observed in both ambient and TME screening conditions. Furthermore, serial exhaustion studies where TANK cells were repeatedly stimulated with tumor cells show sustained cytolytic activity, in contrast to non-TME adapted NK92 counterparts. TANK cells also exhibit higher levels of granzyme B and perforin as assessed by flow cytometry, while exhibiting distinct gene expression signatures as profiled with RNAseq. This initial study supports the hypothesis that immune cells can both react and adapt to different microenvironments. TME-adaptation strategies during cell expansion can enhance potency and efficacy of cell therapies designed to work in a solid tumor microenvironment. Citation Format: Ann Lu, Yunmin Li, Albert Wong, James Lim. Adaptation of therapeutic NK cell line to tumor microenvironment culture conditions increases potency and reduces cellular exhaustion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2763.
Abstract 1882: Passenger gene co-amplification leads to collateral vulnerabilities in cancer
Authors: Yi Bei, Marieluise Kirchner, Luca Brame, Raphaela Fritsche-Guenther, Julia Koeppke, Anja Heeren-Hagemann, Philipp Mertins, Jan Dörr, Anton George Henssen
Journal: Cancer Research (2022)

Abstract The activation of oncogenes via genomic amplification is a hallmark of the cancer genomes, yet such amplifications frequently also encompass neighboring genes. Such passenger genes are involved in essential cellular activities. We hypothesized that co-amplification of passenger genes create cancer-specific collateral therapeutic vulnerabilities. To test this, we analyzed one of the most commonly amplified gene locus near MYCN, which is amplified in nearly 25% of neuroblastoma and around 5% of all cancers. We observed that DDX1, a DEAD-Box helicase, is the most frequently co-amplified passenger gene in MYCN-amplified cancers. Using CRISPR/Cas9 loss-of-function screen results from the Cancer Dependency Map across 739 human cancer cell lines, we reveal that cells with DDX1 co-amplification are highly dependent on the mTOR complex 1(mTORC1). Mechanistically, western blot and immunoprecipitation analyses shows that DDX1 expression leads to higher mTORC1 pathway activity through the interaction between DDX1 and alpha-ketoglutarate dehydrogenase(alpha-KGDH) in mitochondria. DDX1 hijacks alpha-KGDH complex, thereby impairing the function of the Krebs cycle by interfering with the conversion of alpha-ketoglutarate to succinyl-coA. Live cell metabolomics shows accumulated alpha-ketoglutarate in turn activates mTORC1 pathway to promote the ATP production via oxidative phosphorylation(OXPHOS) to maintain cell survival. Consequently, interference with mTORC1 function reduced ATP production and led to accumulated alpha-KG leading to cell death, specifically in DDX1 expressing cells. This suggests that co-amplification of a passenger gene can result in collateral vulnerabilities in cancers, which has the potential to transform future therapeutic target discovery in oncology. Citation Format: Yi Bei, Marieluise Kirchner, Luca Brame, Raphaela Fritsche-Guenther, Julia Koeppke, Anja Heeren-Hagemann, Philipp Mertins, Jan Dörr, Anton George Henssen. Passenger gene co-amplification leads to collateral vulnerabilities in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1882.
Abstract 1090: Repurposing an overactive bladder drug to treat chemoresistant lung cancer
Authors: Joslyn Bassett, Tyler Bland
Journal: Cancer Research (2022)

Abstract Background: Non-small cell lung cancer (NSCLC) is one of the most common types of cancer diagnosis among men and women leads the most cancer-related deaths in the United States. This is largely due to treatment failure which arises from therapy-resistant tumors. The current study investigates the role of muscarinic acetylcholine receptor 3 (CHRM3) in the development and treatment of NSCLC chemotherapy-resistance and the potential of the overactive bladder CHRM3 antagonist darifenacin to treat this lethal form of cancer. Methods: Human NSCLC cell cultures were used to harvest protein for Western blot analyses of protein expression and activity of intracellular pathways. The chemotherapy drug docetaxel’s (DTX) ability to induce apoptosis was measured with crystal violet survival assay and colony formation assay. Results: CHRM3 expression was measured in chemonaive NSCLC cells (A549) and chemoresistant cells (A549R), which showed increased expression in A549R cells. Chemoresistant A549R were pretreated with the CHRM3 antagonist darifenacin (Dari, 10 μM, 24 hrs) before treatment with DTX (48 hrs). Crystal violet survival assay and colony formation assays showed a significant reduction in cell survival in the Dari + DTX combination treatment group suggesting that CHRM3 signaling is necessary in a chemoresistant state. Chemonaive A549 cells and CHRM3 overexpressing A549 cells (A549 M3OE) were pretreated with carbachol (10 µM, 24 hrs) to activate CHRM3 before treatment with a set of serial dilutions of DTX (48 hrs). Crystal violet survival assay results showed that carbachol was not able to protect either cell line from DTX-induced cell death, suggesting that CHRM3 signaling alone is not sufficient to induce a chemoresistant state. Conclusion: CHRM3 overexpression is observed in chemoresistant forms of NSCLC. While activation of CHRM3 does not instill a resistant state in chemonaive cells, its signaling is essential for maintenance of the chemoresistant state. The repurposing of the CHRM3 antagonist darifenacin shows strong potential as a therapeutic to treat lethal chemoresistant forms of NSCLC.The project described was supported by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under Grant #P20GM103408 Citation Format: Joslyn Bassett, Tyler Bland. Repurposing an overactive bladder drug to treat chemoresistant lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1090.
Abstract 2291: microRNA/mRNA integrated analysis of multiple myeloma transcriptomics
Authors: Srinivas V. Koduru
Journal: Cancer Research (2022)

Abstract Myeloma is plasma cell disorder, mostly effects adults over 60 years. Non-coding RNAs are emerging field and play vital role in development of disease. Major non-coding RNAs are miRNAs, lncRNAs, circRNAs and sn/snoRNAs. We analyzed restricted and publically available RNA-seq and small RNA-seq data sets for biomarkers identification and their involvement in myeloma. We obtained restricted data from “BluePrint”, which contains 11 myeloma plasma cells and 4 normal tonsil plasma cells (EGAS00001001110). We identified 1534 genes are differentially regulated (2-fold cut-off, &amp;gt;10-FC 218 genes). Top 10 upregulated genes were: EDNRB (1246-FC), SCUBE1 (737-FC), MC4R (691-FC), NDNF (601-FC), PTGS2 (567-FC), GPRC5D (531-FC), MFAP3L (467-FC), CCND1 (381-FC), CXCL12 (344-FC) and BTBD3 (326-FC) ; top 10 downregulated were: EBF1 (-111-FC), HLA-DRB1(-133-FC), CPXM1 (-171-FC), LOC642131 (-171-FC), IGHV1OR15-3 (-171-FC), HLA-DRB5 (-204-FC), PRAMENP (-210-FC), DTX1 (-220-FC), CD22 (-337-FC) and RFTN1 (-356-FC). Publically available small RNA-seq data downloaded and analyzed for miRNAs, lncRNAs, circRNAs and sn/snoRNAs which contains 3 healthy donor’s plasma cells and 3 newly diagnosed myeloma patient plasma cells (PRJNA377345). We used mirDIP portal to analyze miRNA and mRNA differentially expressed data, predicated from more than 13 databases showed major role of miR-152-3p (targets 28 mRNAs), miR-93-5p (targets 19 mRNAs), miR-301a-3p (targets 13 mRNAs), miR-29c-3p (targets 12 mRNAs), and miR-144-3p (targets 9 mRNAs). Integrated analysis can provide valuable information from the transcriptomics data and effect of miRNAs on mRNAs. Citation Format: Srinivas V. Koduru. microRNA/mRNA integrated analysis of multiple myeloma transcriptomics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2291.
Comparison of dietary and physical activity behaviors in women with and without polycystic ovary syndrome: a systematic review and meta-analysis of 39 471 women
Authors: Maryam Kazemi, Joy Y Kim, Cynthia Wan, Julia D Xiong, Julia Michalak, Isabella B Xavier, Kiran Ganga, Chau Thien Tay, Jessica A Grieger, Stephen A Parry, Lisa J Moran, Marla E Lujan
Journal: Human Reproduction Update (2022)

Lifestyle (dietary and/or physical activity [PA]) modification is recommended as first-line therapy to manage polycystic ovary syndrome (PCOS). Current recommendations are based on healthy lifestyle practices for the general public since evidence for unique lifestyle approaches in PCOS is limited and low quality.
Abstract 3663: Allostatic load, tumor genomics, and outcomes in NSCLC
Authors: Ryan H. Nguyen, Michael Weinfeld, Mary Pasquinelli, Frank Weinberg, Natalie Reizine, Lawrence Feldman, Vijayakrishna K. Gadi
Journal: Cancer Research (2022)

Abstract Introduction: Allostatic load (AL) is a multi-system measure of chronic stress shown to be an emerging framework for understanding disparities in cancer outcomes, but there have been no AL studies in lung cancer. Methods: We conducted a retrospective review of patients diagnosed with stage IV lung adenocarcinoma from 2016 - 2020 at the University of Illinois Hospital and Health System. An AL index included 9 biomarkers (systolic blood pressure, diastolic blood pressure, resting heart rate, BMI, albumin, eGFR, creatinine, glucose, and use of medications for hypertension, diabetes, or hypocholesteremia) with 1 point assigned for each biomarker meeting a pre-determined cutoff. AL was dichotomized between AL-high (5-9) and AL-low (0-4) with median progression-free survival of first-line therapy (mPFS1) and median overall survival (mOS) estimated for both groups with Kaplan-Meier curves. Rates of clinically actionable driver mutations (driver-POS), including EGFR, ALK, ROS1, BRAF V600e, RET, MET, NTRK, and KRAS G12C, were compared for both groups using chi-squared test. Mean AL was compared between those who were driver-POS and those who did not have a clinically actionable driver mutation (driver-NEG) using independent samples t-test. Results: A total of 61 patients were identified with 56% female and 74% former or current tobacco users. The cohort was 49% Black, 21% White, and 13% Hispanic or Latino. Mean AL at diagnosis was 3.3 (+/- 1.4). AL-high patients comprised 20% (12) of the cohort compared with 80% (49) AL-low. Between AL-high and AL-low cohorts, there was no statistically significant difference in mPFS1 (15 vs. 13 months, P = 0.98) and mOS (34 vs. 18 months, P = 0.33). Rates of driver-POS were lower in AL-high compared with AL-low (25% vs 69%, P &amp;lt;0.01). Mean AL was higher in the driver-NEG population compared with driver-POS population (3.79 vs 3.03, P = 0.04). Conclusions: Patients whose tumors did not have a clinically actionable driver mutation were associated with a higher AL, suggestive of higher chronic stress playing a role in more aggressive tumor biology. No statistically significant survival difference was observed in AL-high versus AL-low populations for mPFS1 and mOS. Larger, prospective trials are planned to correlate AL at diagnosis with clinical and biomarker data. AL, which serves as a measure of physiological dysfunction due to chronic stress associated with social disadvantage, may have implications for tumor biology and clinical outcomes in lung cancer. Citation Format: Ryan H. Nguyen, Michael Weinfeld, Mary Pasquinelli, Frank Weinberg, Natalie Reizine, Lawrence Feldman, Vijayakrishna K. Gadi. Allostatic load, tumor genomics, and outcomes in NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3663.
Abstract 535: Development of a liquid biopsy assay to longitudinally monitor changes in mutations’ allelic frequency in response to treatment with KB-0742
Authors: Suha Naffar-Abu Amara, Christina Noe, Tressa Hood, Sara Paganini, Crystal MacKenzie, Melinda A. Day, Pavan Kumar
Journal: Cancer Research (2022)

Abstract Liquid biopsies analyzing cell-free DNA (cfDNA) released by tumors are emerging as a powerful noninvasive sampling approach. As opposed to single-site solid tumor biopsy, liquid biopsies allow for better representation of the tumor mutational landscape. In the clinic, liquid biopsies are utilized for early detection of disease, to help inform treatment decisions, to monitor for disease recurrence, and to identify potential resistance mechanisms. Here we describe our approach to developing a liquid biopsy assay that will allow us to monitor, in real time, longitudinal changes in mutations’ allelic frequency in patients with solid tumors. Our approach combines two powerful technologies: next-generation sequencing, that enables the identification of a broad array of mutations, and droplet digital PCR (ddPCR) that provides speed and a cost-effective advantage to monitor mutations in cfDNA obtained from patient plasma samples. In order to maximize the effectiveness of using liquid biopsy assays in our clinical trial, we prioritized developing an approach that enabled us to meet the following criteria: 1) generating a baseline and end-of-treatment mutational profile for each patient using either a tumor tissue sample or liquid biopsy to identify both driver and potential resistance mutation markers, 2) longitudinal sampling and real-time analysis over the course of treatment, 3) high assay sensitivity to detect low frequency alleles, 4) overall cost-effectiveness, and 5) ability to examine allelic frequency of multiple mutations of interest from limited input of cfDNA isolated from plasma. Assay development included custom quantification of cfDNA and optimization of a pre-amplification step, which amplified the material allowing us to analyze multiple mutations of interest while ensuring that the quantitative nature of the assay was not impacted. For each individual mutation, gBlocks™ and/or cell-line−derived cfDNA were utilized to optimize annealing temperature and time, cycle number, and input amount to attain an assay with a target 0.1% limit of detection. These customized mutation assays can potentially serve as an accelerated cost-effective surrogate approach, compared to imaging, to monitor in real time the response to KB-0742 (CDK9i) in the ongoing phase 1/2 clinical trial NCT04718675. Citation Format: Suha Naffar-Abu Amara, Christina Noe, Tressa Hood, Sara Paganini, Crystal MacKenzie, Melinda A. Day, Pavan Kumar. Development of a liquid biopsy assay to longitudinally monitor changes in mutations’ allelic frequency in response to treatment with KB-0742 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 535.